As anyone following genomics knows, the times they are a’changing again and again, so this is less and less state-of-the-art. So we have decided to try a new course plan this year, taking advantage of the progress in bacterial genome sequencing with long PacBio reads.

“Hopefully” because PacBio on bacteria is not yet routine, depending on the genus and the growth conditions. We are thus trying two different bacteria, a Pseudomonas which has a cool story for the RNA-seq part, and a Caulobacter which has been shown to work with PacBio. Preliminary studies on the Pseudomonas are somewhat discouraging for the PacBio sequencing, but we will still try, with adaptations of the protocol. We will also keep the possibility to reverting to Illumina sequencing plus assembly, but we would like to avoid that (if Caulobacter is plan B, this is plan C).

And of course, we have never done RNA-seq with master students, so this year will be a new adventure, comparable to our first course in 2010. Stressful and exciting. 🙂